\name{geneAnswersConceptNet}
\alias{geneAnswersConceptNet}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Concept-Gene Networking Plotting }
\description{
  A function to generate a concept-gene network by given gene information
}
\usage{
geneAnswersConceptNet(x, colorValueColumn = NULL, centroidSize = c("pvalue", "geneNum", "foldChange", "oddsRatio", "correctedPvalue"), output = c("fixed", "interactive", "none"), showCats=c(1:5), geneLayer=1, edgeM=NULL, catTerm=FALSE, geneSymbol=FALSE, catID=FALSE, nameLength='all', ...)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{x}{ a GeneAnswers instance. }
  \item{colorValueColumn}{ number or column name of geneInput slot to specify the colors of leaves }
  \item{centroidSize}{ type to represent the size of concepts. }
  \item{output}{ output type of final output. }
  \item{showCats}{ a numeric or string vector specified categories  }
  \item{geneLayer}{ an integer, specify how many layers of genes connecting to concepts}
  \item{edgeM}{ a 2-column Matrix representing a network  }
  \item{catTerm}{ a logic value to specify whether mapping category IDs to category names }
  \item{geneSymbol}{ a logic value to specify whether mapping gene IDs to gene symbols }
  \item{catID}{ a logic value to specify whether show category IDs when catTerm is set to TRUE }
  \item{nameLength}{ show how many first letters for long term names, 'all' for full name} 
  \item{\dots}{ other parameters used by 'geneConceptNet' }
}
\details{
  colorValueColumn specifies which column of the geneInput of the GeneAnswers instance is used for color of nodes.
  centroidSize could be one of "geneNum", "pvalue", "foldChange", "oddsRatio", "correctedPvalue". Each one defines to which the size of cencept dot is proportional
  geneNum: number of genes connecting to the concept
  pvalue: p value of enrichment test
  foldChange: fold of gene overrepresent in concepts
  oddsRatio: odds ratio of enrichment test	
  correctedPvalue: adjusted p value of enrichment test
  output defines whether the final figure is interactive or not. Interactive figure calls igraph package to generate a tck/tk canvas. Fixed figure is a non-interactive png figure. None will not output any figure but a list. 
See details in \code{\link{geneConceptNet}} 
}
\value{
  One concept-gene figure is generated. It could be a R figure or tcltk figure depends on how the user set parameter output. 
}
\references{ Feng, G., Du, P., Krett, N., Tessel, M., Rosen, S., Kibbe, W.A. and Lin, S.M., 'A collection of bioconductor methods to visualize gene-list annotations', BMC Research Notes 2010, 3:10}
\author{ Gang Feng, Pan Du and Simon Lin }
\seealso{ \code{\link{getMultiLayerGraphIDs}}, \code{\link{geneConceptNet}} }
\examples{
example(GeneAnswers)
\dontrun{geneAnswersConceptNet(x, colorValueColumn='foldChange', centroidSize='pvalue', output='interactive')}
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{ methods }